Regional campaing’s results (PhD Chapter 1)

1. Maps
- 1.1. General map
- 1.2. Parameters maps
2. Figures

This series of files compile all analyses done during Chapter 1 for the regional campaign (2016).

All analyses have been done with PRIMER-e 6 and R 3.6.0.

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Caracteristics of each campaign

		2014	2016	2017
Sampling date		August-September	June to August	July
Criteria for perturbation		Potentially impacted if close to the city or industries, References outside the bay	Human-impacted if in a region with a highly populated area, industries and maritime activities, Reference if none of these criteria	Human-impacted if in a region with a highly populated area, industries and maritime activities, Reference if none of these criteria
Regions considered		BSI	BSI, CPC, BDA, MR	BSI, MR
Number of sampled stations		40 (20 HI, 20 R)	78 (26 BSI, 19 CPC, 18 BDA, 15 MR)	126 (111 BSI, 15 MR)
Parameters sampled	Organic matter	yes	yes	yes
	Photosynthetic pigments	no	yes	yes
	Sediment grain-size	yes	yes	yes
	Heavy-metals	yes	yes (for a limited number of stations)	no (interpolated based on 2014 and 2016 values)
Benthic communities	Compartment targeted	Macro-infauna	Macro-infauna	Macro-infauna
	Sieved used	500 µm	1 mm	500 µm and 1 mm
	Conservation technique	Formaldehyle	Formaldehyle	Formaldehyle
Others		N.A.	N.A.	N.A.

We used data from subtidal ecosystems (see metadata files for more information). Only stations that have been sampled both for abiotic parameters and benthic species were included.

Selected variables for the analyses:

Depth of the station: depth (only for ANCOVAs)
Percentage of organic matter: om
Percentage of gravel: gravel
Percentage of sand: sand
Percentage of silt: silt
Percentage of clay: clay
Concentration of arsenic: arsenic
Concentration of cadmium: cadmium
Concentration of chromium: chromium
Concentration of copper: copper
Concentration of iron: iron
Concentration of manganese: manganese
Concentration of mercury: mercury
Concentration of lead: lead
Concentration of zinc: zinc
Species richness: S
Abundance of total individuals: N
Shannon index: H
Piélou evenness: J

Abundances of Mesodesma arctatum (Marc) and Cistenides granulata (Cgra) were also considered (see IndVal and SIMPER results).

As data is missing for metal concentrations outside BSI, two Designs have been used:

Design 1: stations at BSI, CPC, BDA, MR with habitat parameters
Design 2: stations at BSI with heavy metal concentrations.

Statistics for each variable considered:

BSI, CPC, BDA, PR (without heavy metals)
	Min	Max	Median	Mean	SD	SE	95% CI
depth	1.000	65.900	16.100	21.131	17.504	1.982	3.884
om	0.168	3.863	0.387	0.689	0.730	0.083	0.162
gravel	0.000	0.809	0.000	0.049	0.122	0.014	0.027
sand	0.000	1.001	0.873	0.707	0.348	0.039	0.077
silt	0.000	0.942	0.031	0.200	0.285	0.032	0.063
clay	0.000	0.497	0.006	0.043	0.098	0.011	0.022
S	0.000	13.000	4.000	4.795	2.969	0.336	0.659
N	0.000	142.000	12.000	19.846	25.867	2.929	5.740
H	0.000	2.307	1.069	1.080	0.610	0.069	0.135
J	0.000	1.000	0.838	0.724	0.292	0.033	0.065

BSI (only heavy metals)
	Min	Max	Median	Mean	SD	SE	95% CI
arsenic	0.800	21.300	2.750	4.188	4.582	0.899	1.761
cadmium	0.080	0.270	0.145	0.152	0.047	0.009	0.018
chromium	17.000	111.000	42.500	49.385	23.565	4.621	9.058
copper	2.400	28.800	6.450	9.373	7.593	1.489	2.919
iron	21938.100	85408.600	42304.650	45356.633	16635.601	3262.510	6394.402
manganese	318.400	1657.100	711.450	776.662	348.066	68.261	133.790
mercury	0.007	0.091	0.019	0.023	0.017	0.003	0.006
lead	1.900	12.200	4.750	5.381	2.902	0.569	1.115
zinc	26.900	141.400	46.800	58.262	29.368	5.760	11.289

1. Maps

1.1. General map

1.2. Parameters maps

For maps of heavy metal concentrations, stations have been grouped based on Environment Canada (2007) classification of sediment toxicity (grey = low toxicity, red = high toxicity).

OM

Gravel

Sand

Silt

Clay

Arsenic

Cadmium

Chromium

Copper

Iron

Manganese

Mercury

Lead

Zinc

Cgra

Marc

Epar

Species richness

Total abundance

Shannon index

Piélou’s evenness

2. Figures

2.1. Barplots

Two types of barplots are available: one for the means by region, and one for the means by depth class. The latter have been done by classifying stations along three groups, based on their depth: shallow (0-10 m), medium (10-25 m) and deep (> 25 m). These thresholds are not supported by evidence, but allow to get a balanced design (26 stations for each depth class). However, we have been using PERMANOVA with depth as a covariate, instead of using these classes as a third factor.

Heavy metals are not presented here, as they were only sampled at BSI stations.

By regions

Organic matter

Grain-size

Species abundances

Diversity indices

By depth classes

Organic matter

Grain-size

Species abundances

Diversity indices

2.2. Phylum frequencies

Phylum abundances by region
Phylum	BSI	CPC	BDA	MR
Annelida	214	69	188	43
Mollusca	191	45	89	100
Arthropoda	119	13	30	43
Echinodermata	27	206	24	138
Platyhelminthes	3	0	0	0
Nematoda	2	0	0	0
Nemertea	1	0	0	0
Brachiopoda	0	0	0	2
Cnidaria	0	0	0	1
Hemichordata	0	0	0	0
Phoronida	0	0	0	0